LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -31.468736 0.0000000) to (3.1465590 31.468736 3.1465590) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.1465590 3.1465590 3.1465590 Created 21 atoms using lattice units in orthogonal box = (0.0000000 -31.468736 0.0000000) to (3.1465590 31.468736 3.1465590) create_atoms CPU = 0.001 seconds 21 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.1465590 3.1465590 3.1465590 Created 21 atoms using lattice units in orthogonal box = (0.0000000 -31.468736 0.0000000) to (3.1465590 31.468736 3.1465590) create_atoms CPU = 0.000 seconds 21 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 1 19 1 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 40 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_486450342170_001#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 1 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.383 | 4.383 | 4.383 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -272.39972 0 -272.39972 -263.12559 1 0 -272.39991 0 -272.39991 -264.65408 Loop time of 0.0117076 on 1 procs for 1 steps with 40 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -272.399717723914 -272.399717723914 -272.399910097338 Force two-norm initial, final = 0.10924030 0.032084038 Force max component initial, final = 0.075344015 0.018043720 Final line search alpha, max atom move = 1.0000000 0.018043720 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.011404 | 0.011404 | 0.011404 | 0.0 | 97.41 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0001099 | 0.0001099 | 0.0001099 | 0.0 | 0.94 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0001937 | | | 1.65 Nlocal: 40.0000 ave 40 max 40 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1460.00 ave 1460 max 1460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2560.00 ave 2560 max 2560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2560 Ave neighs/atom = 64.000000 Neighbor list builds = 0 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 1 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 1 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.383 | 4.383 | 4.383 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1 0 -272.39991 0 -272.39991 -264.65408 623.13342 2 0 -272.39991 0 -272.39991 -114.10987 623.09805 Loop time of 0.0118292 on 1 procs for 1 steps with 40 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -272.399910097338 -272.399910097338 -272.399912105909 Force two-norm initial, final = 0.093622224 0.033784245 Force max component initial, final = 0.062192184 0.017914282 Final line search alpha, max atom move = 0.016079191 0.00028804716 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.011408 | 0.011408 | 0.011408 | 0.0 | 96.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00010553 | 0.00010553 | 0.00010553 | 0.0 | 0.89 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003153 | | | 2.67 Nlocal: 40.0000 ave 40 max 40 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1460.00 ave 1460 max 1460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2560.00 ave 2560 max 2560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2560 Ave neighs/atom = 64.000000 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 1 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.521 | 4.521 | 4.521 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -272.39991 0 -272.39991 -114.10987 Loop time of 6.345e-06 on 1 procs for 0 steps with 40 atoms 189.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 6.345e-06 | | |100.00 Nlocal: 40.0000 ave 40 max 40 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1460.00 ave 1460 max 1460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2560.00 ave 2560 max 2560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2560 Ave neighs/atom = 64.000000 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 1 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.521 | 4.521 | 4.521 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -272.39991 -272.39991 3.1464696 62.937472 3.1464696 -114.10987 -114.10987 20.389517 -383.10864 20.389517 2.7248525 1.6122558e-05 Loop time of 6.565e-06 on 1 procs for 0 steps with 40 atoms 228.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 6.565e-06 | | |100.00 Nlocal: 40.0000 ave 40 max 40 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1460.00 ave 1460 max 1460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 1280.00 ave 1280 max 1280 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2560.00 ave 2560 max 2560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2560 Ave neighs/atom = 64.000000 Neighbor list builds = 0 Dangerous builds = 0 40 -272.399912105909 eV 2.72485247573899 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00